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- PDB-9s3t: Gephyrin dimer of dimers - combined CryoEM map -

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Basic information

Entry
Database: PDB / ID: 9s3t
TitleGephyrin dimer of dimers - combined CryoEM map
ComponentsIsoform 5 of Gephyrin
KeywordsSTRUCTURAL PROTEIN / scaffolding protein / postsynaptic density / protein-protein interaction / linker-mediated regulation
Function / homology
Function and homology information


Molybdenum cofactor biosynthesis / glycine receptor clustering / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase activity / nitrate reductase activity / molybdopterin molybdotransferase activity / molybdopterin adenylyltransferase / molybdopterin molybdotransferase / gamma-aminobutyric acid receptor clustering ...Molybdenum cofactor biosynthesis / glycine receptor clustering / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase activity / nitrate reductase activity / molybdopterin molybdotransferase activity / molybdopterin adenylyltransferase / molybdopterin molybdotransferase / gamma-aminobutyric acid receptor clustering / postsynaptic specialization / inhibitory synapse / Mo-molybdopterin cofactor biosynthetic process / glycinergic synapse / molybdopterin cofactor binding / postsynaptic specialization, intracellular component / response to metal ion / neurotransmitter receptor localization to postsynaptic specialization membrane / synaptic transmission, GABAergic / protein targeting / synapse assembly / synaptic membrane / establishment of protein localization / tubulin binding / GABA-ergic synapse / cytoplasmic side of plasma membrane / molecular adaptor activity / dendritic spine / cytoskeleton / protein-macromolecule adaptor activity / postsynaptic membrane / postsynaptic density / postsynapse / signaling receptor binding / neuronal cell body / dendrite / ATP binding / metal ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Molybdenum cofactor biosynthesis proteins signature 2. / Molybdenum cofactor biosynthesis proteins signature 1. / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily / Molybdopterin biosynthesis protein MoeA-like / MoeA N-terminal region (domain I and II) / MoeA C-terminal region (domain IV) / Molybdenum cofactor biosynthesis, conserved site ...Molybdenum cofactor biosynthesis proteins signature 2. / Molybdenum cofactor biosynthesis proteins signature 1. / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily / Molybdopterin biosynthesis protein MoeA-like / MoeA N-terminal region (domain I and II) / MoeA C-terminal region (domain IV) / Molybdenum cofactor biosynthesis, conserved site / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsOrtiz-Lopez, D. / Hove, T. / Boettcher, B. / Schindelin, H.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research Foundation (DFG)232550447 Germany
German Research Foundation (DFG)456578072 Germany
German Research Foundation (DFG)359471283 Germany
German Research Foundation (DFG)525040890 Germany
CitationJournal: Nat Commun / Year: 2026
Title: Cryo-EM structures of higher order Gephyrin oligomers reveal principles of inhibitory postsynaptic scaffold organization.
Authors: Diego Ortiz-López / Tamsanqa T Hove / Christiane Huhn / Serena Camuso / Pia M van Gen Hassend / Bodo Sander / Benjamin F N Campbell / Shiva K Tyagarajan / Andreas Plückthun / Christian G ...Authors: Diego Ortiz-López / Tamsanqa T Hove / Christiane Huhn / Serena Camuso / Pia M van Gen Hassend / Bodo Sander / Benjamin F N Campbell / Shiva K Tyagarajan / Andreas Plückthun / Christian G Specht / Hans M Maric / Bettina Böttcher / Hermann Schindelin /
Abstract: Gephyrin, the principal scaffolding protein of inhibitory postsynaptic densities, clusters glycine and GABA receptors via multivalent interactions. It features structured N and C terminal domains ...Gephyrin, the principal scaffolding protein of inhibitory postsynaptic densities, clusters glycine and GABA receptors via multivalent interactions. It features structured N and C terminal domains connected by an intrinsically disordered linker. Although the structural and functional properties of its terminal domains are well characterized, the mechanism by which full-length gephyrin organizes into higher-order complexes remains unresolved. Here, we combine biochemical reconstitution, cryo-electron microscopy, and mutational analyses to elucidate the structural logic of gephyrin oligomerization. We demonstrate that gephyrin adopts a stable dimeric assembly which constitutes the basic unit for both linear and oblique tetramers as well as linear hexameric arrangements. High resolution structures reveal a critical segment of the flexible linker that adopts two distinct conformations, one of which occludes the receptor-binding site. This segment harbors key phosphorylation sites, suggesting a regulatory control mechanism. Our findings redefine the architecture of inhibitory postsynaptic sites and reconcile gephyrin oligomerization models with published in-situ postsynaptic densities characterized by cryo-electron tomography.
History
DepositionJul 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 5 of Gephyrin
B: Isoform 5 of Gephyrin
C: Isoform 5 of Gephyrin
D: Isoform 5 of Gephyrin


Theoretical massNumber of molelcules
Total (without water)326,8934
Polymers326,8934
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Isoform 5 of Gephyrin / Putative glycine receptor-tubulin linker protein


Mass: 81723.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gphn, Gph / Production host: Escherichia coli (E. coli) / Strain (production host): DE3
References: UniProt: Q03555, molybdopterin adenylyltransferase, molybdopterin molybdotransferase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Gephyrin E-domain homotetramer in Gephyrin full length context
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.35 MDa / Experimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: DE3
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMSodium chlorideNaCl1
35 mM2-mercaptoethanolC2H6OS1
41 mMEDTAC10H16N2O81
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingAverage exposure time: 1.1 sec. / Electron dose: 42.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5particle selection
2PHENIX1.21.2_5419:model refinement
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.48 Å / Resolution method: OTHER / Num. of particles: 283182 / Details: Combined map / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312993
ELECTRON MICROSCOPYf_angle_d0.53717681
ELECTRON MICROSCOPYf_dihedral_angle_d4.9541800
ELECTRON MICROSCOPYf_chiral_restr0.0442063
ELECTRON MICROSCOPYf_plane_restr0.0042337

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